Genomic Epidemiology Analysis

What You Can Achieve

• De novo genome assembly and gene annotation
• Comprehensive screening for resistance, virulence, and mycotoxin genes
• Strain typing using MLST or cgMLST
• Detection of single nucleotide variants (SNVs) and insertions/deletions (InDels)
• Functional interpretation of genomic variation

Before You Start

We support your project from design to data interpretation. Consider these key points:

• Is a reference genome available for your organism?
• Are MLST profiles established for this species?
• Do you expect large structural variants or rearrangements?
• Could contamination or complex microbial communities be present?
• Are there specific resistance or virulence genes you wish to track?

Modular Workflow

Outsource the entire workflow—or select specific modules. Our process is designed for flexibility. Typical workflow steps include:

Bioinformatic Analysis

Gain actionable insights across all key aspects of genomic epidemiology:

Strain Relationship & Typing

• What is the phylogenetic relationship to known strains?
• What MLST or cgMLST profile does the isolate match?

Resistance, Virulence & Mycotoxins

• Which functional genes are present in the genome?

Variant Analysis

• What SNVs and InDels are detected, and what are their predicted effects?

Microbial Community Profiling (if applicable)

• What species or strains are present, and in what abundance?

Gene Discovery

• Are novel genes present that share homology with known protein families?

You receive comprehensive raw and processed data along with visual summaries—ready for downstream research or publication.

Turnaround Time

• 20 working days for sequencing
• +5 working days for full analysis
• Express service available upon request

Sample Requirements

• Buffer recommendation: 10 mM Tris-HCl (pH 7.5–8.5)
• Important: Avoid any buffers containing EDTA >1mM
• DNA quantification: Use fluorometric methods (e.g., PicoGreen®, Qubit®)

Minimum Input for Illumina Libraries